ArticleBMC bioinformatics2013
Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- GenPTM: A Generalizable Framework for Protein Post-Translational Modification Information Extraction from the Scientific Literature.Research square · 2026Article
- Article
- GlycoSiteMiner: an ML/AI-assisted literature mining-based pipeline for extracting glycosylation sites from PubMed abstracts.Glycobiology · 2025Article
- A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability.Angewandte Chemie (International ed. in English) · 2024Article
- Current Approaches in Supersecondary Structures Investigation.International journal of molecular sciences · 2021Review
- LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome.Cell · 2021Article
- Triage by ranking to support the curation of protein interactions.Database : the journal of biological databases and curation · 2017Article
- Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.CEUR workshop proceedings · 2016Article
- The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track.Database : the journal of biological databases and curation · 2016Article
- Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.Database : the journal of biological databases and curation · 2015Article
- Extracting rate changes in transcriptional regulation from MEDLINE abstracts.BMC bioinformatics · 2014Article
- Towards precision medicine: advances in computational approaches for the analysis of human variants.Journal of molecular biology · 2013Review
- RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB.
resultsThe procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments.
conclusionsThe information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.
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